Figure 1
From: An enhanced RNA alignment benchmark for sequence alignment programs
MAFFT (FFT-NS-2) and ClustalW performance with optimized and old parameters. PROALIGN (earlier identified to be a good aligner [22]) is included as a reference. Performance is measured as BRALISCORE vs. reference APSI and exemplified for k = 5 sequences. MAFFT version 5.667 was used with optimized parameters, which are default in version 5.667, and with (old) parameters of version 4, respectively; CLUSTALW was used either with default parameters or with optimized parameters (see Table 2 and text).